Digital Commons Network^™

Ai-Marrvel - A Knowledge-Driven Ai System For Diagnosing Mendelian Disorders, Dongxue Mao, Chaozhong Liu, Linhua Wang, Rami Ai-Ouran, Cole Deisseroth, Sasidhar Pasupuleti, Seon Young Kim, Lucian Li, Jill A Rosenfeld, Linyan Meng, Lindsay C Burrage, Michael F Wangler, Shinya Yamamoto, Undiagnosed Diseases Network, Michael Santana, Victor Perez, Priyank Shukla, Christine M Eng, Brendan Lee, Bo Yuan, Fan Xia, Hugo J Bellen, Pengfei Liu, Zhandong Liu

Faculty, Staff and Students Publications

BACKGROUND: Diagnosing genetic disorders requires extensive manual curation and interpretation of candidate variants, a labor-intensive task even for trained geneticists. Although artificial intelligence (AI) shows promise in aiding these diagnoses, existing AI tools have only achieved moderate success for primary diagnosis.

METHODS: AI-MARRVEL (AIM) uses a random-forest machine-learning classifier trained on over 3.5 million variants from thousands of diagnosed cases. AIM additionally incorporates expert-engineered features into training to recapitulate the intricate decision-making processes in molecular diagnosis. The online version of AIM is available at https://ai.marrvel.org. To evaluate AIM, we benchmarked it with diagnosed patients from three independent cohorts.

RESULTS: AIM …

The Effects Of Ammonia On The Functionality Of Bovine Granulosa Cells, Micah Henrie

All Graduate Theses and Dissertations, Fall 2023 to Present

It is common practice in the livestock animal production industries to feed high levels of protein to maximize the yield of each animal in production. However, diets high in protein can cause decreased reproductive success within these animals. The causes behind this decrease are not fully understood. Increased dietary protein leads to increased levels of both ammonia and urea in the blood of the animal. These increased metabolite levels may be a possible explanation for the decline in reproductive success. The goal of this study is to identify how various levels of ammonia affect the function of bovine granulosa cells …

Generative Ai In Education From The Perspective Of Students, Educators, And Administrators, Aashish Ghimire

All Graduate Theses and Dissertations, Fall 2023 to Present

This research explores how advanced artificial intelligence (AI), like the technology that powers tools such as ChatGPT, is changing the way we teach and learn in schools and universities. Imagine AI helping to summarize thick legal documents into something you can read over a coffee break or helping students learn how to code by offering personalized guidance. We looked into how teachers feel about using these AI tools in their classrooms, what kind of rules schools have about them, and how they can make learning programming easier for students. We found that most teachers are excited about the possibilities but …

Achieving Responsible Anomaly Detection, Xiao Han

All Graduate Theses and Dissertations, Fall 2023 to Present

In the digital transformation era, safeguarding online systems against anomalies – unusual patterns indicating potential threats or malfunctions – has become crucial. This dissertation embarks on enhancing the accuracy, explainability, and ethical integrity of anomaly detection systems. By integrating advanced machine learning techniques, it improves anomaly detection performance and incorporates fairness and explainability at its core.

The research tackles performance enhancement in anomaly detection by leveraging few-shot learning, demonstrating how systems can effectively identify anomalies with minimal training data. This approach overcomes data scarcity challenges. Reinforcement learning is employed to iteratively refine models, enhancing decision-making processes. Transfer learning enables the …

A Framework That Explores The Cognitive Load Of Cs1 Assignments Using Pausing Behavior, Joshua O. Urry

All Graduate Theses and Dissertations, Fall 2023 to Present

Pausing behavior in introductory Computer Science (CS1) courses has been related to a student’s performance in the course and could be linked to a student’s cognitive load, or assignment difficulty. Having an objective measure of the cognitive load would be beneficial to course instructors as it would help them design assignments that are not too difficult. Two studies are presented in this work. The first study uses Cognitive Load Theory and Vygotsky’s Zone of Proximal Development as a theoretical framework to analyze pause times between keystrokes to better understand what types of assignments need more educational support than others. The …

Online Deception: The Impact Of Language In Text-Based Deception Detection, Stephanie Dayle Avila

All Graduate Theses and Dissertations, Fall 2023 to Present

In today’s digital age, spreading false information online can have serious consequences, from affecting elections to undermining public health efforts. Despite the issue's importance, there’s been relatively little research into better understanding how people make decisions about lies and misinformation online. My project dives into this challenge by exploring how specific language cues, like grammar errors or unusual word choices, influence people’s perception of statements in terms of deceit online. I examined how people react to these cues through three separate but related studies when reading truthful and deceptive statements. The first two studies showed that true statements with grammatical …

Artificial Intelligence In Landscape Architecture: A Survey Of Theory, Culture, And Practice, Phillip J. Fernberg

All Graduate Theses and Dissertations, Fall 2023 to Present

This dissertation explores the role of artificial intelligence (AI) in shaping the landscape architecture profession. It looks at how AI has evolved in the field, its current influence, and its potential to change research, teaching, and professional practice. The research includes a detailed review of existing literature to identify trends in AI applications and gaps in knowledge. It also examines landscape architects' attitudes towards AI, revealing a mix of enthusiasm for its benefits and concerns about its impact on creativity and design processes, and proposes new ways of thinking about and working with AI. The work brings a unique perspective …

Variations On Leitmotif: Firebird Rises, Virginia Beikmann

All Graduate Theses and Dissertations, Fall 2023 to Present

This thesis begins with an introduction that discusses the various influences on the development of the creative novella portion. These influences include Russia literature and folklore, as well as the genres of alternative history and speculative fiction. The novella takes place in a re-imagining of Moscow, Russia during the 1917 Bolshevik Revolution. The novella portion is driven by a close focus on character, with emphasis on reactions to wartime pressures and interpersonal relationships forming the central conflict.

Nutrient Management Of Cannabis In Controlled Environments, Julie A. Hershkowitz

All Graduate Theses and Dissertations, Fall 2023 to Present

Cannabis has been cultivated for millennia as a multipurpose crop for food, fiber, and medicine. Secondary metabolites called cannabinoids, including cannabidiol (CBD) and the psychoactive Δ-9 tetrahydrocannabinol (Δ-9 THC), are responsible for the medicinal properties of cannabis. The intoxicating nature of THC resulted in legislation prohibiting the possession and production of cannabis within the United States during the 20^th century. As a result, research programs on cannabis production were halted at most institutions. In recent years, cannabis production has become widespread within the US as a result of increasing legalization. However, modern cannabis production nutrient management programs often include …

Understanding Timing Error Characteristics From Overclocked Systolic Multiply-Accumulate Arrays In Fpgas, Andrew S. Chamberlin

All Graduate Theses and Dissertations, Fall 2023 to Present

Artificial Intelligence (AI) is one of the biggest fields of research for computer hardware right now. Hardware accelerators are chips (such as graphics cards) that are purpose built to be the best at a specific type of operation. AI hardware accelerators are a growing field of research. Part of hardware in general is a digital clock that controls the pace at which computations occur. If this clock runs too quickly, the hardware won't have enough time to finish its computation. We call that a timing error. This paper focuses on studying the characteristics of timing errors in a small custom …

Novel Kinetic Description Of Real-Time Polymerase Chain Reaction Characterizes Interrelated Effects Of Sample, Master Mix, And Cycle Time, David Tafur

All Graduate Theses and Dissertations, Fall 2023 to Present

Real-time quantitative polymerase chain reaction fluorescent curves are influenced by the quantification method, template length, primer sequence, polymerase activity, reaction conditions, and unwanted side reactions. Interpretation of these curves depends on understanding the subjacent mechanisms by which those factors can alter the curve profile, particularly on highly diluted analytes or impure samples. However, such factors are individually described today, or their interplay is not fully developed. The present work examines the effect of primer dimer formation and extension, resource competition, template reannealing, and polymerase thermodegradation, in addition to novel descriptions of polymerase competitive inhibition, extended primer amplification, and the probability …

The Last Days Of Elder Mitchell, Jack Bylund

All Graduate Theses and Dissertations, Fall 2023 to Present

The Last Days of Elder Mitchell is a novella following the eponymous Latter-Day Saint missionary as he narrates the miracles performed by his colleague, Elder Gibson, as well as his personal grappling with his queer identity as he serves a high-demand religion that condemns people like him. The narrative explores the intersection of queerness and faith, the form of the novella, and the healing nature of autobiographical fiction.

Predictors And Impact Of Prolonged Vasoplegia After Continuous-Flow Left Ventricular Assist Device Implantation, Harveen K Lamba, Mary Kim, Meng Li, Andrew B Civitello, Ajith P Nair, Leo Simpson, J Patrick Herlihy, O H Frazier, Joseph G Rogers, Gabriel Loor, Kenneth K Liao, Alexis E Shafii, Subhasis Chatterjee

Faculty, Staff and Students Publications

BACKGROUND: Vasoplegia after cardiac surgery is associated with adverse outcomes. However, the clinical effects of vasoplegia and the significance of its duration after continuous-flow left ventricular assist device (CF-LVAD) implantation are less known.

OBJECTIVES: This study aimed to identify predictors of and outcomes from transient vs prolonged vasoplegia after CF-LVAD implantation.

METHODS: The study was a retrospective review of consecutive patients who underwent CF-LVAD implantation between January 1, 2005, and December 31, 2017. Vasoplegia was defined as the presence of all of the following: mean arterial pressure ≤65 mm Hg, vasopressor (epinephrine, norepinephrine, vasopressin, or dopamine) use for >6 hours …

Natural History Of Cancer-Associated Splanchnic Vein Thrombosis, Hanqing Shang, Jun Y Jiang, Danielle Guffey, Francisco Novoa, Raka Bandyo, Shengling Ma, Ang Li

Faculty, Staff and Students Publications

Background: There is uncertainty in the management of cancer-associated isolated splanchnic vein thrombosis (SpVT).

Objectives: To describe the natural history of SpVT by cancer type and thrombus composition and to review anticoagulation (AC) practices and associated rates of usual-site venous thromboembolism (VTE), major and clinically relevant nonmajor bleeding (MB/CRNMB), recanalization/progression, and mortality.

Methods: We performed a retrospective cohort study in patients with SpVT at 2 cancer care centers in Houston, Texas. We estimated the incidence of usual-site VTE and MB/CRNMB at 6 months using competing risk methods and examined venous patency in a subset of patients with repeat imaging. We …

A Parametric Study On The Energy Dissipation Capability Of Frictional Mechanical Metamaterials Engineered For Vibration Isolation, Shayan Khosravi, Mohsen Amjadian

Civil Engineering Faculty Publications

Mechanical metamaterials are engineered structures with complex geometric arrangements that display unconventional mechanical properties which are uncommon in traditional materials. They possess the ability to manipulate and control mechanical wave propagation across specific frequency ranges known as frequency bandgaps. This feature makes them extremely useful for a variety of applications in structural control including passive vibration isolation. These materials can be engineered to selectively block or redirect the input motion at their dominant frequency while allowing the transmission of motion at other frequencies. This paper aims to study the dynamic performance of an innovative mechanical metamaterial designed for seismic isolation …

Rejection, Creation, And Abolitionist Futures: Sustaining Ecosystems Of Care Under Neoliberal Violence 1980-Present, Maya Phelps

Senior Honors Papers / Undergraduate Theses

The enforcement of the child welfare system through policies, funding practices, and ideologies is a national investment in the nuclear family as a critical social institution to the United States (US); this investment communicates to the broader population that conforming to this heteropatriarchal, white supremacist conception of family provides protection from state intervention to those who conform. My project interrogates child welfare’s enforcement of normative families, and the resistance from Black family formations and kinship based on their social position and its relation to power. Focusing on the period between 1980 and the present, I examine the ways Black family …

The Impact Of One Night Of Sleep Restriction On Perception Of Subsequent Aerobic Exercise Performance, Erin G. Meier

Senior Honors Projects, 2020-current

Introduction: Previous research has established that poor sleep quality negatively impacts aerobic exercise performance. A majority of that research has examined extreme sleep disruption like complete sleep deprivation or multiple nights of reduced sleep. Little research exists examining the effect of a singular night of sleep restriction (SR) on performance, and there is even less research on the associated perceptual feelings and outcomes from SR that may influence performance. Previous research from our laboratory has suggested that a single night of SR may impair performance, but did not account for sleep inertia or examine any perceptual factors. Therefore, the …

Improved Test Fixture For Collecting Microcontact Performance And Reliability Data, Turja Nandy, Ronald A. Coutu Jr., Rafee Mahbub

Electrical and Computer Engineering Faculty Research and Publications

Microelectromechanical systems (MEMS) ohmic contact switches are considered to be a promising candidate for wireless communication applications. The longevity of MEMS switches is directly related to the reliability and performance of microcontacts. In this work, an improved microcontact test fixture with high actuation rates (KHz) and highly precise position control (nm) and force (nN) control was developed. Here, we collected microcontact performance data from initial contact tests (ICT) and microcontact reliability data from cold switched tests (CST). To perform these tests with our test fixture, we fabricated MEMS microcontact test structures with relatively high Young’s modulus electroplated Nickel (Ni)-based, fixed–fixed …

Texture-Based Classification To Overcome Uncertainty Between Covid-19 And Viral Pneumonia Using Machine Learning And Deep Learning Techniques, Omar Farghaly, Priya Deshpande

Electrical and Computer Engineering Faculty Research and Publications

The SARS-CoV-2 virus, responsible for COVID-19, often manifests symptoms akin to viral pneumonia, complicating early detection and potentially leading to severe COVID pneumonia and long-term effects. Particularly affecting young individuals, the elderly, and those with weakened immune systems, the accurate classification of COVID-19 poses challenges, especially with highly dimensional image data. Past studies have faced limitations due to simplistic algorithms and small, biased datasets, yielding inaccurate results. In response, our study introduces a novel classification model that integrates advanced texture feature extraction methods, including GLCM, GLDM, and wavelet transform, within a deep learning framework. This innovative approach enables the effective …

Piezo1 Regulates Meningeal Lymphatic Vessel Drainage And Alleviates Excessive Csf Accumulation, Dongwon Choi, Eunkyung Park, Joshua Choi, Renhao Lu, Jin Suh Yu, Chiyoon Kim, Luping Zhao, James Yu, Brandon Nakashima, Sunju Lee, Dhruv Singhal, Joshua P Scallan, Bin Zhou, Chester J Koh, Esak Lee, Young-Kwon Hong

Faculty, Staff and Students Publications

Piezo1 regulates multiple aspects of the vascular system by converting mechanical signals generated by fluid flow into biological processes. Here, we find that Piezo1 is necessary for the proper development and function of meningeal lymphatic vessels and that activating Piezo1 through transgenic overexpression or treatment with the chemical agonist Yoda1 is sufficient to increase cerebrospinal fluid (CSF) outflow by improving lymphatic absorption and transport. The abnormal accumulation of CSF, which often leads to hydrocephalus and ventriculomegaly, currently lacks effective treatments. We discovered that meningeal lymphatics in mouse models of Down syndrome were incompletely developed and abnormally formed. Selective overexpression of …

Effects Of Serum Potassium On Mortality In Patients With St-Elevation Myocardial Infarction, Colton J Jensen, Jonathan K Nielsen, Matthew M Talbott, Danielle O'Connell, Vivek S Patel, Peyton A Armstrong, Zubaid Rafique, Lillian M Tia, Krishna K Paul, Dietrich V Jehle

Faculty, Staff and Students Publications

Introduction: Disturbances in potassium levels can induce ventricular arrhythmias and heighten mortality in patients with ST-elevation myocardial infarction (STEMI). This study evaluates the influence of sK levels on seven-day mortality and incidence of ventricular arrhythmias in STEMI patients to further improve clinical guidelines and outcomes.

Methods: This retrospective, propensity-matched study analyzed approximately 250,000 acute STEMI patients from 55 major academic medical centers/healthcare organizations (HCOs) in the US Collaborative Network of the TriNetX database. The sK levels recorded on the day of STEMI diagnosis were categorized into four cohorts: sK ≤ 3.4 (hypokalemia), 3.5 ≤ sK ≤ 4.5 (normal-control), 4.6 ≤ …

The Interplay Of Casing Material And Detonation Wave Shock Parameters In Steel Witness Plate Dent Formation, Emily M. Johnson, Catherine E. Johnson

Mining Engineering Faculty Research & Creative Works

This Study Uses Both Experimentation and Simulation to Investigate How Varying Casing Material Around Cylindrical Composition-B Charges Affects Witness Plate Response and Diagnoses the Cause of the Differences in the Dents Produced. through Experimentation, It Was Found that Consistent Dents Are Produced from Repeated Tests and Characteristically Different Dents Are Produced by Charges with Different Casing Material. Charges Cased in Viscoelastic Materials Produced Shallower Dents Than Those Without Casing. Simulation Was Validated Against the Experimental Dents, and the Detonation Wave Parameters Were Measured for 25 Differently Cased Charges: 15 Metals and 10 Polymers. Regression Fit Relationships Were Derived Relating Dent …

A Study Of Cybersecurity Landscape In The United States: Trend, Regional Variations, And Socioeconomic Factors, Trang Thi Thu Horn

All-Inclusive List of Electronic Theses and Dissertations

The Internet has become an essential part of our daily lives. Cyberspace has emerged significantly with an enormous number of users, creating a lucrative hunting field for cybercriminals. The exponential growth of internet users and online activities, along with the increased sophistication of cybercrimes, is raising significant global concerns for individuals, organizations, and governments. This research aims to explore the cybersecurity landscape in the United States, investigate regional variations, and the potential impact of the COVID-19 pandemic on the number of cybercrimes. The study utilizes a mixed research method approach, including historical analysis and a Delphi study. Historical analysis studied …

Dimensional Regularization And Two-Loop Vacuum Polarization Operator: Master Integrals, Analytic Results, And Energy Shifts, Stefano Laporta, Ulrich D. Jentschura

Physics Faculty Research & Creative Works

We Present a Complete Reevaluation of the Irreducible Two-Loop Vacuum-Polarization Correction to the Photon Propagator in Quantum Electrodynamics, i.e. with an Electron-Positron Pair in the Fermion Propagators. the Integration is Carried Out by Reducing the Integrations to a Limited Set of Master Integrals, Which Are Calculated using Integration-By-Parts Identities. Dimensional Regularization is Used in D=4-2ϵ Dimensions, and On-Mass Shell Renormalization is Employed. the One-Loop Effect is Given to Order ϵ, to Be Combined with the 1/ϵ Divergence of the Two-Loop Amplitude. Master Integrals Are Given. Final Evaluations of Two-Loop Energy Shifts for 1S, 2S, and 2P States Are Done Analytically, …

Scalar Susceptibility Of A Diluted Classical Xy Model, Reece Beattie-Hauser, Thomas Vojta

Physics Faculty Research & Creative Works

We Analyze the Amplitude Fluctuations in a Diluted 3D Classical XY Model Near the Magnetic Phase Transition, motivated by the Unusual Localization Properties of the Amplitude (Higgs) Mode Recently Found at the Disordered Superfluid-Mott Glass Quantum Phase Transition. We Calculate the Amplitude Correlation Function and the Corresponding Scalar Susceptibility by Means of Monte Carlo Simulations. in Contrast to the Quantum Case, in Which the Scalar Susceptibility Was Found to Violate Naive Scaling, We Find that the Scalar Susceptibility of the Classical System Fulfills Naive Scaling (Employing the Clean Critical Exponents, as Expected from the Harris Criterion) as the Temperature is …

Critical Risk Assessment, Diagnosis, And Survival Analysis Of Breast Cancer, Shamiha Binta Manir, Priya Deshpande

Electrical and Computer Engineering Faculty Research and Publications

Breast cancer is the most prevalent type of cancer in women. Risk factor assessment can aid in directing counseling regarding risk reduction and breast cancer surveillance. This research aims to (1) investigate the relationship between various risk factors and breast cancer incidence using the BCSC (Breast Cancer Surveillance Consortium) Risk Factor Dataset and create a prediction model for assessing the risk of developing breast cancer; (2) diagnose breast cancer using the Breast Cancer Wisconsin diagnostic dataset; and (3) analyze breast cancer survivability using the SEER (Surveillance, Epidemiology, and End Results) Breast Cancer Dataset. Applying resampling techniques on the training dataset …

Characterizing Modulators Of Protease-Activated Receptors With A Calcium Mobilization Assay Using A Plate Reader, Jacob T. Derousse, Chris Dockendorff

Chemistry Faculty Research and Publications

Changes in calcium concentration in cells are rapidly monitored in a high-throughput fashion with the use of intracellular, fluorescent, calcium-binding dyes and imaging instruments that can measure fluorescent emissions from up to 1,536 wells simultaneously. However, these instruments are much more expensive and can be challenging to maintain relative to widely available plate readers that scan wells individually. Described here is an optimized plate reader assay for use with an endothelial cell line (EA.hy926) to measure the protease-activated receptor (PAR)-driven activation of G_αq signaling and subsequent calcium mobilization using the calcium-binding dye Fluo-4. This assay has been used to …

A Comparison Of Post-Operative Pain Management Following Lumbar Laminectomy Fusions Utilizing Tlip Or Intra-Operative Local Anesthesia Block, Lauren Eberhardt, Philip Zakko, Karen Childers, Daniel Park

Conference Presentation Abstracts

Background/Introduction: Spinal fusion patients suffer significant acute post-operative pain, potentially leading to chronic pain. Opioids are commonly used for peri-operative pain management despite significant side effects. The thoracolumbar interfascial plane (TLIP) and erector spinae plane (ESP) block, alternative analgesic options with rare side effects, have proven to reduce pain and opioid consumption compared to standard non-block care. This study aimed to determine if a significant difference exists between block groups with multi- and single level laminectomy fusions in post-operative and discharge opioid consumption and length of stay. Materials/Methods: A retrospective review was performed via data query for lumbar laminectomy fusion …

Diuretic Dose Ratio Is Associated With Reduced Hospital Length Of Stay In Acute Heart Failure, Sarah Galla, Yuying Xing, Lihua Qu, David A. Berger

Conference Presentation Abstracts

Background and Objectives: Congestive heart failure (CHF) is anticipated to affect eight million Americans by 2030. Treatment for CHF exacerbation is centered around IV diuretics. There are no current studies indicating an optimal initial diuretic dose in the Emergency Department (ED), and our objective is to test our hypothesis that higher diuretic dose ratio may shorten hospital length of stay (LOS). Methods: We conducted a retrospective cohort study of a large health system from 2016 to 2022. We included patients admitted from the ED with a primary diagnosis of “CHF exacerbation” with a history of CHF and prescribed diuretics. Exclusions …

Screen Positives For Potential St-Segment Elevation Myocardial Infarction: Door To Electrocardiogram By Sex And Race, Sarah Galla, Gautam Pathak, Dalia Owda, Amit Bahl, James Ziadeh, Susan Bork, Robert Swor, Karen Childers, Maya Yiadom, David A. Berger

Conference Presentation Abstracts

Background and Objectives: Detection of ST-segment elevation myocardial infarctions (STEMI) are dependent on early acquisition of an ECG. American Heart Association guidelines require performing an ECG within 10 min for patients presenting with symptoms warranting STEMI screening. A delay in ECG acquisition causes delays in diagnosis and treatment, which is associated with worsened outcomes. However, previous work has shown there is limited success at achieving a door to ECG (D2E) time of Methods: This is a retrospective chart review study in which D2E time was measured for patients positive for STEMI ECG screening criteria in a large health system with …